[AMBER] Radii in prmtop

From: Jesper Sørensen <jesorensen.ucsd.edu>
Date: Thu, 26 Apr 2012 09:51:48 -0700

Hi All,

I have a question regarding the radii in my prmtop file. I have built my system in tleap with the input file shown below.
I made sure to use tleap -s, so no other input files were pre-loaded.

When I look in my prmtop file it says I am using mbondi2 radii. Which I am a bit confused by.
Looking through the manuals and the literature, ff10 for proteins is equal to Amber99SB. Amber99 uses as far as I can tell the Amber94 radii - by this I mean I haven't seen any updated vdW parameters in the newer force field papers (ff99, ff99SB).
So, should my prmtop file not have the amber94 radii instead of the mbondi radii?

I hope you can clarify this for me a bit.

Best regards,

modified Bondi radii (mbondi)
  1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
  1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00

source leaprc.ff10
addAtomTypes {
        { "O3" "O" "sp2" }
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
loadAmberParams ../ATP/frcmod.phos
loadAmberPrep ../ATP/ATP.prep
ATP = atp
set default FlexibleWater on
mol = loadPdb pdbfile.pdb
solvateBox mol TIP4PEWBOX 10.0
addions mol Na+ 18 Cl- 11
check mol
saveAmberParm mol system.prmtop system.inpcrd
AMBER mailing list
Received on Thu Apr 26 2012 - 10:00:02 PDT
Custom Search